Update on Delta and other Variants in South Africa - Prof Tulio de Oliveira and Dr. Richard Lessells, KRISP for the Network for Genomic ...
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Update on Delta and other Variants in
South Africa
Prof Tulio de Oliveira and Dr. Richard Lessells, KRISP
for the Network for Genomic Surveillance South Africa (NGS-SA)
UKZN INSPIRING GREATNESS
Daily Cases / Weekly Excess Deaths
10000
15000
20000
25000
5000
0
SA
24−Feb
09−Mar
23−Mar
06−Apr
20−Apr
04−May
18−May
01−Jun
15−Jun
29−Jun
13−Jul
27−Jul
10−Aug
24−Aug
07−Sep
21−Sep
05−Oct
19−Oct
02−Nov
16−Nov
30−Nov
14−Dec
28−Dec
11−Jan
25−Jan
08−Feb
phase (Re >1)
22−Feb
08−Mar
UKZN INSPIRING GREATNESS
22−Mar
05−Apr
19−Apr
03−May
17−May
31−May
14−Jun
28−Jun
12−Jul
0
1
2
3
Re
South Africa has entered exponential growth
Proportion of Genomes
0.00
0.25
0.50
0.75
1.00
17−Feb−2020
02−Mar−2020
16−Mar−2020
30−Mar−2020
13−Apr−2020
27−Apr−2020
11−May−2020
25−May−2020
08−Jun−2020
22−Jun−2020
06−Jul−2020
20−Jul−2020
03−Aug−2020
17−Aug−2020
31−Aug−2020
14−Sep−2020
28−Sep−2020
12−Oct−2020
26−Oct−2020
Date
09−Nov−2020
23−Nov−2020
07−Dec−2020
21−Dec−2020
04−Jan−2021
18−Jan−2021
01−Feb−2021
15−Feb−2021
01−Mar−2021
15−Mar−2021
UKZN INSPIRING GREATNESS
29−Mar−2021
12−Apr−2021
26−Apr−2021
10−May−2021
24−May−2021
07−Jun−2021
21−Jun−2021
05−Jul−2021
NA
Variants
Detection of Delta in South Africa
21D (Eta)
B.1.1.318
21A (Delta)
21B (Kappa)
Other lineages
20H (Beta, V2)
20I (Alpha, V1)
Variants over time by province
South Africa variants by province
KwaZulu−Natal
Variants
Gauteng
20H (Beta, V2)
Western Cape
20I (Alpha, V1)
Northern Cape
21A (Delta)
North West
21B (Kappa)
Free State
21D (Eta)
Mpumalanga
B.1.1.318
Limpopo
Other lineages
Eastern Cape
Oct Nov Dec Jan Feb Mar Apr May Jun
2020 2020 2020 2021 2021 2021 2021 2021 2021
month
UKZN INSPIRING GREATNESS
Detection of Delta in KZN from community
surveillance
Across six districts and in > 30 random selected sites of KwaZulu-
Natal, Harry Gwala (n=16), Zululand (n=15), iLembe (n=14),
eTheweni (n=12), King Cetshwayo (n=1) and Ugu (n=1)
UKZN INSPIRING GREATNESS
Delta also detected and increasing
prevalence in the Western Cape
Delta was detected in 3/3 samples in the Garden route in late May
UKZN INSPIRING GREATNESS
Very limited data in Gauteng
NICD responsibility, but KRISP has now received samples this Thursday (2
days ago) and will have results by Monday/Tuesday
UKZN INSPIRING GREATNESS
Onset of Illness among the First 425 Confirmed Cases of Novel
Delta mutation
Coronavirus (2019-nCoV)–Infected – spike(NCIP)
profilePneumonia protein
in
Wuhan, China.
Source: Johns Hopkins University
Two mutations in receptor-binding domain (L452R & T478K)
Substitution (T19R) and deletion (157-158del) in N-terminal
domain antigenic supersite
Mutation adjacent to S1/S2 furin cleavage site (P681R)
https://covdb.stanford.edu/page/mutation-viewer/#sec_delta
UKZN INSPIRING GREATNESS
Onset of Illness among the First 425 Confirmed Cases of Novel
Delta global distribution
Coronavirus (2019-nCoV)–Infected Pneumonia (NCIP) in
Wuhan, China.
Source: Johns Hopkins University
First sampled in India October 2020
Now detected in 85 countries, including several in Africa,
and rapidly becoming dominant in many countries
https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports
UKZN INSPIRING GREATNESS
Onset of Illness among the First 425 Confirmed Cases of Novel
CoronavirusSummary of Delta
(2019-nCoV)–Infected variant
Pneumonia (NCIP) in
Wuhan, China.
Source: Johns Hopkins University
Transmissibility Disease severity
Highly transmissible – more than No clear evidence yet
all other variants, including Beta
Risk of reinfection Vaccines
Reduction in neutralization with No evidence of vaccine escape
serum from people infected with High levels of protection against
Beta variant severe disease
UKZN INSPIRING GREATNESSOnset of Illness among the First 425 Confirmed Cases of Novel
Evidence
Coronavirus of increasedPneumonia
(2019-nCoV)–Infected transmissibility
(NCIP) in
Wuhan, China.
Source: Johns Hopkins University
• Preliminary estimates from genomic data and
epidemiological studies suggest Delta may be
significantly more transmissible than other variants of
concern, including Beta (30-60% more transmissible)
• These data imply that Delta could be approximately
twice as transmissible as the earlier non-VOC/VOI
viruses
Campbell F, et al. Eurosurveillance 2021
Allen H, et al. Public Health England preprint
Public Health England Technical Briefings
UKZN INSPIRING GREATNESSOnset of Illness among the First 425 Confirmed Cases of Novel
Clinical presentation
Coronavirus (2019-nCoV)–Infected Pneumonia (NCIP) in
Wuhan, China.
Source: Johns Hopkins University
• Some evidence from UK that symptom profile could
be different – most prominent current symptoms are
headache, sore throat, runny nose and sneezing
• More work needed to confirm if this is a consistent
finding with the Delta variant or reflects clinical profile
of infections in certain age groups and/or in
partially/fully vaccinated individuals
https://covid.joinzoe.com/post/new-top-5-covid-symptoms
UKZN INSPIRING GREATNESSOnset of Illness among the First 425 Confirmed Cases of Novel
Disease severity
Coronavirus (2019-nCoV)–Infected Pneumonia (NCIP) in
Wuhan, China.
Source: Johns Hopkins University
• Early evidence from the UK suggests there may be an
increased risk of hospitalisation within 14 days of a
positive test, compared to contemporaneous cases
with Alpha variant (risk approximately double)
• No evidence currently from the UK of increased case
fatality ratio with Delta variant, but more follow-up of
cases required
Public Health England Technical Briefings
UKZN INSPIRING GREATNESSOnset of Illness among the First 425 Confirmed Cases of Novel
Vaccine effectiveness
Coronavirus (2019-nCoV)–Infected Pneumonia (NCIP) in
UK data – symptomatic disease
Wuhan, China.
Source: Johns Hopkins University
Vaccine Vaccine effectiveness single Vaccine effectiveness two
dose doses
Alpha Delta Alpha Delta
Astra Zeneca 51% (47-55) 33% (19-44) 66% (54-75) 60% (29-77)
Pfizer 49% (43-55) 33% (8-51) 93% (90-96) 88% (78-93)
Compared to Alpha, there was a modest reduction in
effectiveness against symptomatic disease after a single dose,
but very little difference after two doses
Lopez Bernal J, et al. medRxiv 2021
UKZN INSPIRING GREATNESSOnset of Illness among the First 425 Confirmed Cases of Novel
Vaccine effectiveness
Coronavirus (2019-nCoV)–Infected Pneumonia (NCIP) in
UK data – hospitalisation
Wuhan, China.
Source: Johns Hopkins University
Vaccine Vaccine effectiveness single Vaccine effectiveness two
dose doses
Alpha Delta Alpha Delta
Astra Zeneca 76% (61-85) 71% (51-83) 86% (53-96) 92% (75-97)
Pfizer 83% (62-93) 94% (46-99) 95% (78-99) 96% (86-99)
These findings suggest high levels of protection (>70%) against
hospitalisation with the Delta variant with one or two doses of
either vaccine – levels of protection similar to the Alpha variant
Stowe J, et al. PHE preprint 2021
UKZN INSPIRING GREATNESSSummary
• Delta is now rapidly becoming the dominant SARS-CoV-2 variant in
many countries around the world, including SA
• There is now good evidence that Delta is more transmissible than
previously circulating viruses and other variants of concern/interest
• There is some reduction in neutralization with convalescent serum
collected post-Beta infection, raising concerns about potential for re-
infection in SA
• Vaccine effectiveness data from UK suggest good protection against
symptomatic disease, and very high levels of protection against
hospitalization, after two doses of Pfizer or Astra Zeneca vaccine and
seems effective agains J&J
UKZN INSPIRING GREATNESSOnset of Illness among the First 425 Confirmed Cases of Novel
CoronavirusSummary of Delta
(2019-nCoV)–Infected variant
Pneumonia (NCIP) in
Wuhan, China.
Source: Johns Hopkins University
Transmissibility Disease severity
Highly transmissible – more than No clear evidence yet
all other variants, including Beta
Risk of reinfection Vaccines
Reduction in neutralization with No evidence of vaccine escape
serum from people infected with High levels of protection against
Beta variant severe disease
UKZN INSPIRING GREATNESSNetwork for Genomic Surveillance in South
Africa (NGS-SA)
Supported by the DSI and the SA MRC
Msomi N, Mlisana K, et al. Lancet Microbe 2020
UKZN INSPIRING GREATNESSImpact
Onset onamong
of Illness antibody
the Firstneutralization &ofrisk
425 Confirmed Cases Novel
Coronavirus (2019-nCoV)–Infected Pneumonia (NCIP) in
Wuhan, China. of reinfection
Source: Johns Hopkins University
Non-VOC/VOI sera
• Reduced neutralization of Delta by
convalescent serum from people
infected early in epidemic, but not
as marked as the reduction
observed with Beta
• However, significant reduction in
neutralization of Delta by
Beta sera convalescent serum from people
infected with Beta variant
• Raises concern that people with
prior Beta infection could be
susceptible to reinfection with Delta
Liu C, et al. Cell 2021
UKZN INSPIRING GREATNESSOnset of Illness among the First 425 Confirmed Cases of Novel
Impact(2019-nCoV)–Infected
Coronavirus on neutralization by vaccines
Pneumonia (NCIP) in
Wuhan, China.
Source: Johns Hopkins University
Pfizer vaccine
• Reduced neutralization of Delta by
serum from people post-Pfizer
and Astra Zeneca vaccine,
compared to early circulating
strain
• However, reduction in
neutralization of Delta less
Astra Zeneca vaccine pronounced than for Beta (for both
vaccines)
• No neutralization data yet for
Johnson & Johnson vaccine
Liu C, et al. Cell 2021
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